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SSRN 2024年

作者： Frigaard, Niels-Ulrik Seemann, Stefan E. Marine Biological Section Department of Biology University of Copenhagen Helsingør Denmark Center for non-coding RNA in Technology and Health Department of Veterinary and Animal Sciences University of Copenhagen Frederiksberg Denmark

Methane (CH4) and carbon dioxide (CO2) occur as undesirable waste products in carbon-based fuel productions. Bothgases are major greenhouse gases with CH4 being much more potent than CO2. For this reason, excess CH4 from varioussources is often flared into CO2 rather than releasing the CH4 into the atmosphere, however, some CH4 is still emitteddue to the inefficiency of flare combustion. We have explored how natural microbial communities can be manipulatedinto consuming both CH4 and CO2 from a gas stream and converting the gases into microbial biomass. Natural seawaterwas enriched with inorganic nutrients and injected with a continuous gas stream containing CH4 (4.7% v/v) and CO2(1% v/v) over a period of several days, either in the dark or in the light. Microbial communities established thatcontained methanotrophic bacteria consuming CH4, and cyanobacteria and microalgae consuming CO2. The measureof chemotaxonomic markers revealed that the growth of phototrophs increased greatly only in the light with an earlydominance by cyanobacteria later overtaken by microalgae, and that the growth of methanotrophs increased greatlyonly in the dark. The microbial communities were characterized using near-full-length 16S/18S rrna gene ampliconsequencing with the Nanopore technology. In the incubated cultures, the microbial diversity was drastically lower ascompared to the natural communities. The most abundant microalgae were green algae belonging to Picochlorum,Tetraselmis, Chlamydomonas, and Nannochloris, and the most abundant cyanobacteria were related to Geitlerinemasp. PCC 7105, Symphothece sp. PCC 7002 and Cyanobium sp. PCC 6307 (based on the SILVA reference database).Methylomicrobium and Methylobacter were the most abundant methanotrophs in the dark-incubated cultures, whereasMethylomonas methanica was identified as the single methanotroph with notable abundance under light ***, for optimal CH4 and CO2 consumption it may be necessary to physically separate

关键词： Microalgae

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Discovering and Evaluating Organizational Knowledge from Textual Data: Application to Crisis Management

SSRN

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SSRN 2023年

作者： Grissa, Dhouha Andonoff, Eric Hanachi, Chihab Center for non-coding RNA in Technology and Health Department of Veterinary and Animal Science University of Copenhagen Frederiksberg C1870 Denmark Université Toulouse - Capitole IRIT 2 rue du Doyen Gabriel Marty Toulouse31042 France

Crisis management effectiveness relies mainly on the quality of the distributed human organization deployed for saving lives, limiting damage and reducing risks. Organizations set up in this context are not always predefined and static;they could evolve and new forms could emerge since actors, such as volunteers or NGO, could join dynamically to collaborate. To improve crisis resolution effectiveness, it is first important to understand, analyze and evaluate such dynamic organizations in order to adjust crisis management plans and ease coordination among actors. Giving a textual experience feedback from past crisis, the objective of this paper is to discover the organizational structure deployed in the considered crisis and then evaluate it according to a set of criteria. For that purpose, we combine in a coherent framework text and association rule mining for pattern discovery and annotation, and multi-agent system models and techniques for formally building and evaluating organizational structures. We present the OSminer algorithm that discovers association rules based on relevant textual patterns and then builds an organizational structure including three main relations between actors: power, control and coordination. A real-life case study, a flood crisis hitting the south west of France, serves as a basis for testing/experimenting our solution. The organizational structure, discovered in this case study, has 24 actors. Its evaluation indicates its efficiency, but shows that it is neither robust nor flexible. Our findings highlight the potential of our approach to discover and evaluate organizational structures from a text recording interactions between stakeholders in a crisis context. © 2023, The Authors. All rights reserved.

关键词： Association rules

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Inhibition of KDM6B prevents osteoarthritis by blocking growth plate-like H3K27me3 loss in bivalent genes

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Science China Life Sciences 2025年第5期68卷 1423-1436页

作者： Hao Du Yao Zhang Xi Yu Xuanhe You Diwei Wu Ze Du Yongrui Cai Zhenyu Luo Hanpeng Lu Zhixin Liao Bi-Sen Ding Ya Zhao Yan Wang Ke Xiao Fan Yang Fangji Gan Ning Ning Jiancheng Zeng Peiliang Shi Zongke Zhou Shishu Huang Department of Orthopedic Surgery and Orthopedic Research Institute West China HospitalSichuan University Rehabilitation Medicine Center West China HospitalSichuan University Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE State Key Laboratory of BiotherapyWest China Second University HospitalSichuan University Institute of Translational Medicine Medical CollegeYangzhou University Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research College of Animal Science and Technology Sichuan Agricultural University Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province Sichuan Agricultural University Department of Lower Limb Surgery of Sichuan Province Orthopedic Hospital Central Laboratory of Sichuan Province Orthopedic Hospital Brain Cognition and Brain Disease Institute (BCBDI) Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions School of Mechanical Engineering Sichuan University Gem Pharmatech (Chengdu) Co. Ltd.

Osteoarthritis(OA) is the most prevalent joint disorder occurring with articular cartilage degradation. It includes a switch from an articular to a growth plate chondrocyte phenotype. Here, we investigated the histone modification profiles and found significant H3K27me3 loss in OA, which led to disease-associated gene expression. Surprisingly, these genes were occupied by both H3K27me3 and H3K4me3 in normal chondrocytes, showing a poised bivalent state. Furthermore, we observed the derepression of similar bivalent genes in growth plate chondrocytes. Finally, a KDM6B inhibitor GSK-J4 prevented the H3K27me3 loss and cartilage damage in the rat OA model. Our results reveal an inherited bivalent epigenetic signature on developmental genes that makes articular chondrocytes prone to hypertrophy and contributes to a promising epigenetic therapy for OA.

关键词： osteoarthritis histone modifications H3K27me3 bivalency growth plate

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Using GPU to accelerate the pairwise structural rna alignment with base pair probabilities

Using GPU to accelerate the pairwise structural RNA alignmen...

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作者： Sundfeld, Daniel Teodoro, George Havgaard, Jakob H. Gorodkin, Jan Melo, Alba C. M. A. Information and Communication Technology Brasília Federal Institute Brasília Brazil Department of Computer Science University of Brasília Brasília Brazil Center for Non-Coding RNA in Technology and Health Department of Veterinary and Animal Sciences University of Copenhagen Copenhagen Denmark

Structural alignments of Ribonucleic acid (rna) sequences solved by the Sankoff algorithm are computationally expensive and often require constraints to be used in practice. Modern Graphics Processing Units (GPUs) contain more than 1000 cores, which compute in parallel to speed up applications. Here, we present a GPU-based solution to the rna structural alignment problem that makes use of precalculated base pair probabilities on the individual sequences. We designed and developed an unconstrained version of the Sankoff algorithm, obtaining the optimal result and calculating the entire four-dimension dynamic programming matrix (4D DP). Our approach uses a two-level wavefront strategy to exploit parallelism. The 4D DP matrix is divided in one external matrix (EM) and several internal matrices (IM). We applied wavefront strategies on the EM and IMs in a two-level hierarchical way. At the first level, the wavefront is applied to the EM, calculating the cells that belong to the same diagonal in parallel. In the second level, since each cell in the EM is itself an IM matrix, the cells that belong to the same IM diagonal are calculated in parallel. The results obtained with real rna sequences show that our GPU version is capable of outperforming a multicore CPU version of the unconstrained version of the Sankoff algorithm. Compared with the CPU-based version running on 32 cores, our approach is able to achieve a speedup of 7.81x on the NVidia Tesla P100. In this case, the execution time was reduced from 6 hours and 18 minutes (32 cores) to 48 minutes and 20 seconds (GPU). © 2019 John Wiley & Sons, Ltd.

关键词： Graphics processing unit

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Double-network hydrogel enhanced by SS31-loaded mesoporous polydopamine nanoparticles:Symphonic collaboration of near-infrared photothermal antibacterial effect and mitochondrial maintenance for full-thickness wound healing in diabetes mellitus

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Bioactive Materials 2023年第9期27卷 409-428页

作者： Qing-Song Deng Yuan Gao Bi-Yu Rui Xu-Ran Li Po-Lin Liu Zi-Yin Han Zhan-Ying Wei Chang-Ru Zhang Fei Wang Helen Dawes Tong-He Zhu Shi-Cong Tao Shang-Chun Guo Department of Orthopedic Surgery Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine600 Yishan RoadShanghai200233China School of Medicine Shanghai Jiao Tong University227 South Chongqing RoadShanghai200025China Institute of Microsurgery on Extremities Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine600 Yishan RoadShanghai200233China Department of Rheumatology The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical UniversityNo.29XinglongxiangTianning DistrictChangzhou213000China Shanghai Clinical Research Centre of Bone Diseases Department of Osteoporosis and Bone DiseasesShanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233China Shanghai Key Laboratory of Orthopedic Implants Department of Orthopedic SurgeryShanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineNo.639 Zhizaoju RoadShanghai200011China Clinical and Translational Research Center for 3D Printing Technology Medical 3D Printing Innovation Research CenterShanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai200125China Department of Orthopedics Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin Second RoadShanghai200025China Faculty of Health and Life Science Oxford Brookes UniversityHeadington RoadOxfordOX30BPUK NIHR Oxford Health Biomedical Research Centre OxfordOX37JXUK College of Medicine and Health St Lukes CampusUniversity of ExeterHeavitree RoadExeterEX12LUUK School of Chemistry and Chemical Engineering Shanghai Engineering Research Center of Pharmaceutical Intelligent EquipmentShanghai Frontiers Science Research Center for Druggability of Cardiovascular Non-Coding RNAInstitute for Frontier Medical TechnologyShanghai University of

Diabetic wound healing has become a serious healthcare *** high-glucose environment leads to persistent bacterial infection and mitochondrial dysfunction,resulting in chronic inflammation,abnormal vascular function,and tissue *** solve these issues,we developed a double-network hydrogel,constructed with pluronic F127 diacrylate(F127DA)and hyaluronic acid methacrylate(HAMA),and enhanced by SS31-loaded mesoporous polydopamine nanoparticles(MPDA NPs).As components,SS31,a mitochondria-targeted peptide,maintains mitochondrial function,reduces mitochondrial reactive oxygen species(ROS)and thus regulates macrophage polarization,as well as promoting cell proliferation and migration,while MPDA NPs not only scavenge ROS and exert an anti-bacterial effect by photothermal treatment under near-infrared light irradiation,but also control release of SS31 in response to *** F127DA/HAMA-MPDA@SS31(FH-M@S)hydrogel has characteristics of adhesion,superior biocompatibility and mechanical properties which can adapt to irregular wounds at different body sites and provide sustained release of MPDA@SS31(M@S)*** addition,in a diabetic rat full thickness skin defect model,the FH-M@S hydrogel promoted macrophage M2 polarization,collagen deposition,neovascularization and wound ***,the FH-M@S hydrogel exhibits promising therapeutic potential for skin regeneration.

关键词： Mesoporous polydopamine nanoparticles(MPDA NPs) SS31 Photothermal antibacterial Mitochondrial function maintenance Diabetic wound healing

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The Theory of Gene Family Histories

arXiv

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arXiv 2023年

作者： Hellmuth, Marc Stadler, Peter F. Department of Mathematics Faculty of Science Stockholm University StockholmSE - 106 91 Sweden Bioinformatics Group Department of Computer Science Interdisciplinary Center for Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Fraunhofer Institute for Cell Therapy and Immunology Perlickstraße 1 LeipzigD-04103 Germany Institute for Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Center for Non-coding RNA in Technology and Health University of Copenhagen Grønnegårdsvej 3 Frederiksberg CDK-1870 Denmark Santa Fe Institute 1399 Hyde Park Rd Santa FeNM87501 United States

Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is the broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes. Copyright © 2023, The Authors. All rights reserved.

关键词： Genes

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A novel tissue engineered nerve graft constructed with autologous vein and nerve microtissue repairs a longsegment sciatic nerve defect

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Neural Regeneration Research 2021年第1期16卷 143-149页

作者： Jing Wang Ya-Qiong Zhu Yu Wang Hong-Guang Xu Wen-Jing Xu Yue-Xiang Wang Xiao-Qing Cheng Qi Quan Yong-Qiang Hu Chang-Feng Lu Yan-Xu Zhao Wen Jiang Chen Liu Liang Xiao Wei Lu Chen Zhu Ai-Yuan Wang Spine Research Center of Wannan Medical College Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution(Wannan Medical College)Department of Spine SurgeryYijishan HospitalThe First Affiliated Hospital of Wannan Medical CollegeWuhuAnhui ProvinceChina Department of Ultrasound Chinese PLA General HospitalBeijingChina Department of Orthopedic Surgery Key Laboratory of Musculoskeletal Trauma&War Injuries PLABeijing Key Lab of Regenerative Medicine in OrthopedicsChinese PLA General HospitalBeijingChina Medical College of Nankai University TianjinChina The Neural Regeneration Co-Innovation Center of Jiangsu Province NantongJiangsu ProvinceChina Department of Anesthesiology the Second Affiliated Hospital of Inner Mongolia Medical UniversityHuhhotInner Mongolia Autonomous RegionChina Department of Orthopedic Surgery Yan’an University Affiliated HospitalYan’anShaanxi ProvinceChina Department of Orthopedic Surgery the First Affiliated Hospital of Medical CollegeShihezi UniversityShiheziXinjiang Uygur Autonomous RegionChina Department of Orthopedic Surgery The First Peoples’Hospital of Yunnan ProvinceKunmingYunnan ProvinceChina Department of Orthopedic Surgery Anhui Provincial HospitalThe First Affiliated Hospital of University of Science and Technology of ChinaHeifeiAnhui ProvinceChina

Veins are easy to obtain,have low immunogenicity,and induce a relatively weak inflammatory ***,veins have the potential to be used as conduits for nerve ***,because of the presence of venous valves and the great elasticity of the venous wall,the vein is not conducive to nerve *** this study,a novel tissue engineered nerve graft was constructed by combining normal dissected nerve microtissue with an autologous vein graft for repairing 10-mm peripheral nerve defects in *** with rats given the vein graft alone,rats given the tissue engineered nerve graft had an improved sciatic static index,and a higher amplitude and shorter latency of compound muscle action ***,rats implanted with the microtissue graft had a higher density and thickness of myelinated nerve fibers and reduced gastrocnemius muscle atrophy compared with rats implanted with the vein ***,the tissue engineered nerve graft had a lower ability to repair the defect than autogenous nerve *** summary,although the tissue engineered nerve graft constructed with autologous vein and nerve microtissue is not as effective as autologous nerve transplantation for repairing long-segment sciatic nerve defects,it may nonetheless have therapeutic potential for the clinical repair of long sciatic nerve *** study was approved by the Experimental Animal Ethics Committee of Chinese PLA General Hospital(approval No.2016-x9-07)on September 7,2016.

关键词： in vivo injury motor neurological function peripheral nerve injury rat recovery regeneration repair

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Computational Discovery of Conserved rna Structures and Functional Characterization of a Structured lncrna in Leishmania braziliensis

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non-coding rna Research 2025年

作者： Caroline R. Espada Christian Anthon Rubens D.M. Magalhães José Carlos Quilles Junior Natalia M.M. Teles Fabiano S. Pais Lissur A. Orsine Letícia de Almeida Tânia P.A. Defina Adam Dowle Jan Gorodkin Pegine B. Walrad Angela K. Cruz Department of Cell and Molecular Biology Ribeirão Preto Medical School University of São Paulo FMRP-USP Ribeirão Preto São Paulo Brasil Department of Biology York Biomedical Research Institute University of York York United Kingdom Center for non-coding RNA in Technology and Health Department of Animal and Veterinary Sciences Faculty for Health and Medical Sciences University of Copenhagen Copenhagen Denmark Data Science Lab Metabolomics and Proteomics Lab Bioscience Technology Facility Department of Biology University of York York United Kingdom

Leishmania parasites alternate between hosts, facing environmental changes that demand rapid gene expression adaptation. Lacking canonical rna polymerase II promoters, transcription in these eukaryotes is polycistronic, with gene regulation occurring post-transcriptionally. Although non-coding rnas (ncrnas) have been identified in Leishmania transcriptomes, their functions remain unclear. Recognizing rna structure's importance, we performed a genome-wide alignment of L. braziliensis and related species, identifying conserved rna structures, 38 of which overlap with known ncrnas. One such ncrna, lncrna45 , was functionally characterized. Using a knockout cell line, we demonstrated that lncrna45 is crucial for parasite fitness. Reintroducing the wild type lncrna45 restored fitness, while a version with a single nucleotide substitution in the structured region did not. This mutation also altered rna-protein interactions. These findings suggest that lncrna45 's regulatory role and protein interactions rely on its secondary structure. This study highlights the significance of structured lncrnas in Leishmania biology and their potential as therapeutic targets. Further research into these ncrnas could uncover new parasite regulation mechanisms and inspire novel treatment strategies.

关键词： non-coding rnas Leishmania braziliensis rna structure Gene expression regulation CRISPR- Cas9

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DNA origami technology for biomedical applications: Challenges and opportunities

MedComm - Biomaterials and Applications

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MedComm - Biomaterials and Applications 2023年第2期2卷

作者： Li, Ling Nie, Shihong Du, Ting Zhao, Jiaxuan Chen, Xiaoyuan West China School of Public Health West China Fourth Hospital and State Key Laboratory of Biotherapy Sichuan University Chengdu China Department of Radiation Oncology Cancer Center West China Hospital Sichuan University Chengdu China Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province Chengdu Medical College Chengdu China Departments of Diagnostic Radiology Surgery Chemical and Biomolecular Engineering and Biomedical Engineering Yong Loo Lin School of Medicine and Faculty of Engineering National University of Singapore Singapore Singapore Clinical Imaging Research Centre Centre for Translational Medicine Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore Nanomedicine Translational Research Program NUS Center for Nanomedicine Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR) Singapore Singapore

DNA origami, a promising branch of structural DNA technology, refers to the technique of folding a single-stranded DNA scaffold into well-defined nanostructures. In recent years, DNA origami nanostructures have shown considerable promise in a variety of biomedical applications, owing to their biodegradability, unique programmability, and addressability. Despite their popularity, the biomedical application of DNA origami techniques, which exploits their unique programmability and addressability, is rare in previous studies. Most recently, mounting evidence has demonstrated the robustness of DNA origami nanostructures in the spatial organization of functional components at the nanoscale in the biomedical field. These examples provide typical paradigms to fully realize the potential of DNA origami techniques by taking advantage of their unique programmability and addressability. This minireview summarizes the recent advancements of DNA origami techniques in biosensing, biocatalysis, and drug delivery, and the representative examples using DNA origami nanostructures for the spatial organization of functional molecules with nanometric precision are highlighted. We further discuss the possible limitations and challenges for in vivo applications, including stability issues and potential immunogenicity, and finally, propose some strategies to overcome these obstacles to fully realize the potential of DNA origami techniques in biomedical applications. © 2023 The Authors. MedComm – Biomaterials and Applications published by John Wiley & Sons Australia, Ltd on behalf of Sichuan International Medical Exchange & Promotion Association (SCIMEA).

关键词： biocatalysis biosensing DNA nanotechnology DNA origami

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PTMD: A Database of Human Disease-associated Post-translational Modifications

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 244-251页

作者： Haodong Xu Yongbo Wang Shaofeng Lin Wankun Deng Di Peng Qinghua Cui Yu Xue Department of Bioinformatics & Systems Biology MOE Key Laboratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering Huazhong University of Science and Technology Department of Biomedical Informatics School of Basic Medical Sciences MOE Key Laboratory of Molecular Cardiovascular Sciences Center for Non-coding RNA Medicine Peking University

Various posttranslational modifications （PTMs） participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM–disease associations （PDAs）would be a great help for both academic research and clinical use. In this work, we reported PTMD,a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of diseaseassociated PTM events. By reconstructing a disease–gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http：//***.

关键词： Posttranslational modification Phosphorylation PTM-disease association Disease-gene network AKT1

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